I have a suspicion that if you disconnect the trans command your problem may stop. I own and have "looked" at several of Bills diesel tunes all of them had modified trans controls written in. I think they are conflicting with each other.
Very generally speaking in simplified terms.
Both the transcomode and Bills written in trans controls provide more clamping pressure to the clutch packs in certain circumstances to prevent slipping / put more powa to da ground. Moving a from a dead stop, decelerating and the OD shift creates the highest pump pressures. IMO.
My WAG is the pulsing occurs during the lag time difference between the electric command signal from the PCM to the trans to do something verses the mechanical time it takes to dump the extreme pressure caused by the dual trans controls.
The chattering you notice is the trans acting upon the engine during the time it takes to dump the pressure and release the clutches.
Or it could be the torque converter itself, the 99's were famous for being noisy, increased pressure makes it worse.
Or I could be wrong.
Dang, I just noticed how old this post is.